Setting your species (number of chromosomes, chromosome length) Recombination only happens *between* markers in this simulation, so if you have chromosome "beyond" the last marker, that region is never going to have a recombination. There should be a marker at the beginning and end of the chromosome.Each chromosome should probably have at least 5 or 10 markers on it. If, for example, you have only two markers on a whole chromosome, then you are limited to one recombination for the entire chromosome. There can only be one recombination between markers in the simulation, so markers must be fairly closely spaced.Information about the Marker Description File: The name of this file can be anything, but you will have to specify it by editing the UserDefined.pm file ( instructions). This file contains the names and locations of markers. Marker description file (tab delimited spreadsheet).Spreadsheet configuration file (tab delimited spreadsheet).This file contains the information about how many chromosomes animals of this species have, how long each chromosome is, and what breeding scheme is to be executed.If they are not saved as tab-delimited files, Genome Mixer will be totally unable to read them, and may give you cryptic errors. If you use Excel or some other spreadsheet program to edit this file, you should be sure to export it as a tab-delimited file. Note: The following two spreadsheet files should be saved as tab-delimited spreadsheet files. Under normal circumstances, this is the only Perl file that you will want to edit. UserDefined.pm - user-defined variables (names of input/output files, etc).Perl source file to be edited by the end user (you):
Selection.pm - selection by genotype (favorable, lethal alleles, etc)this is NOT yet incorporated completely into GenomeMixer.MouseCell.pm - aggregates mice together, for litters.Mouse.pm - stores the data for each mouse.MarkerCollection.pm - deals with the marker data after it is read in from the user-specified file.(instead of storing a thousand "A"s from position 0 to 1000, we store the "generange" "") GeneRange.pm - specs for "gene ranges," which are used to represent "runs" of genetic data.Chromosome.pm - specs for the chromosome objects.You will NOT need to edit this file all the user-defined configuration options are in the " UserDefined.pm" file. You run Genome Mixer by running this Perl fileall of the other files are referred to from this file. The files that make up the entire Genome Mixer package: You can use it with just about any animal, however, if you change the number and length of the chromosomes. Genome Mixer is a Perl program designed for simulating mouse breeding experiments. Fixing input files / perl files (linebreak issues).
Bbedit remember window position mac os x#
on Mac OS X / Linux / Unix (only OS X documentation, currently)
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